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Table 1 Data sets from GEO database

From: Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments

N GEO data set Experiment summary/Title N A N B N PC N Ka
1 GSE8441 Study of whether inadequate protein intake differentially affects skeletal muscle transcript levels and expression profiles in older adults[24] 11 11 9 5
2 GSE9499 DNA methyltransferase 3B (DNMT3B) mutations in ICF syndrome[25] 15 7 77 6
3 GSE2638 and 2639 GSE2639: HUVEC were left untreated or stimulated for 5h with 2 ng/ml TNF. Comparsion of the gene profiles revealed TNF-mediated gene expression changes in HUVEC[26]. Study TNF stimulated vs controls. 7 7 13 8
4 GSE2638 and 2639 GSE2638: HMEC cultures were left untreated or stimulated for 5h with 2 ng/ml TNF. Comparison of the gene expression profiles revealed the TNF-mediated gene expression changes[26]. Study HMEC vs HUVEC 3 4 16 9
5 GSE3860 Comparison of Hutchinson–Gilford Progeria Syndrome fibroblast cell lines to control fibroblast cell lines[27]. 9 9 8 11
6 GSE6344 Gene expression in Stage 1,2 Normal and Tumor kidney cancer[28] 10 10 19 15
7 GSE7765 Dioxin-induced gene expression changes in MCF-7 human breast cancer cells[29] 3 3 13 18
8 GSE6740_1 Comparison of transcriptional profiles of CD4+ and CD8+ T cells from HIV-infected patients and uninfected control group[30]. Study of CD4+ T cells 10 10 40 24
9 GSE6740_2 Comparison of transcriptional profiles of CD4+ and CD8+ T cells from HIV-infected patients and uninfected control group[30]. Study of CD8+ T cells 10 10 62 25
10 GSE6011 Expression data from quadriceps muscle of young DMD patients and age matched controls[31] 14 23 10 30
11 GSE2531 Total RNA from two commonly used choriocarcinoma cell lines, JEG3 and BeWo, are compared in this experiment to identify differentially expressed transcripts[32]. 3 4 17 36
  Total N P     284  
  1. Data sets from GEO database[33], used for testing efficiency of DFC test. Samples in all data sets were profiled on Affymetrix GeneChip HG-U133A microarrays with 22283 probesets. Shortcuts: N A – number of samples in condition A, N B – number of samples in condition B, N PC – number of probesets checked by RT PCR. Total number of probesets, checked by RT PCR is 284. For easy access for data set’s detailed information we provide in the last column N Ka – data set’s number in the description file of ref[9].